MZ ratios

M/Z ratios: Mass hysteria ensues

Before we run our samples on the mass spectrometer, we need to know what mass-to-charge ratios (m/z ratios) to use. By looking at the output m/z ratios of previous runs, we can assess which range to use. To do this, I examined Rhonda’s larval Crassostrea gigas mass spectrometer results.

Previous runs were generally saved on Emma’s database, which allows the user to search mass spectrometer output using a handy web interface. However, Rhonda’s data is saved on our lab computer Emu. This made the process of extracting and manipulating the files I needed convoluted. With some lab teamwork, we figured it out!

Here’s the final protocol:

Using this R script, I randomly selected 10 of Rhonda’s samples to work with. The files I need to work with are the ones named interact..pep.xml

I used the following code to manipulate the pep.xml file of interest. The code manipulates TPP viewer through the command line and allows me to export the data file as an .xls document.